Jangam Annie P, Pathak Ravi R, Raghuram Nandula
University School of Biotechnology, Guru Gobind Singh Indraprastha University Dwarka, India.
Front Plant Sci. 2016 Jan 28;7:11. doi: 10.3389/fpls.2016.00011. eCollection 2016.
The genome-wide role of heterotrimeric G-proteins in abiotic stress response in rice has not been examined from a functional genomics perspective, despite the availability of mutants and evidences involving individual genes/processes/stresses. Our rice whole transcriptome microarray analysis (GSE 20925 at NCBI GEO) using the G-alpha subunit (RGA1) null mutant (Daikoku 1 or d1) and its corresponding wild type (Oryza sativa Japonica Nipponbare) identified 2270 unique differentially expressed genes (DEGs). Out of them, we mined for all the potentially abiotic stress-responsive genes using Gene Ontology terms, STIFDB2.0 and Rice DB. The first two approaches produced smaller subsets of the 1886 genes found at Rice DB. The GO approach revealed similar regulation of several families of stress-responsive genes in RGA1 mutant. The Genevestigator analysis of the stress-responsive subset of the RGA1-regulated genes from STIFDB revealed cold and drought-responsive clusters. Meta data analysis at Rice DB revealed large stress-response categories such as cold (878 up/810 down), drought (882 up/837 down), heat (913 up/777 down), and salt stress (889 up/841 down). One thousand four hundred ninety-eight of them are common to all the four abiotic stresses, followed by fewer genes common to smaller groups of stresses. The RGA1-regulated genes that uniquely respond to individual stresses include 111 in heat stress, eight each in cold only and drought only stresses, and two genes in salt stress only. The common DEGs (1498) belong to pathways such as the synthesis of polyamine, glycine-betaine, proline, and trehalose. Some of the common DEGs belong to abiotic stress signaling pathways such as calcium-dependent pathway, ABA independent and dependent pathway, and MAP kinase pathway in the RGA1 mutant. Gene ontology of the common stress responsive DEGs revealed 62 unique molecular functions such as transporters, enzyme regulators, transferases, hydrolases, carbon and protein metabolism, binding to nucleotides, carbohydrates, receptors and lipids, morphogenesis, flower development, and cell homeostasis. We also mined 63 miRNAs that bind to the stress responsive transcripts identified in this study, indicating their post-transcriptional regulation. Overall, these results indicate the potentially extensive role of RGA1 in the regulation of multiple abiotic stresses in rice for further validation.
尽管有突变体以及涉及单个基因/过程/胁迫的证据，但尚未从功能基因组学角度研究异源三聚体G蛋白在水稻非生物胁迫响应中的全基因组作用。我们使用Gα亚基（RGA1）缺失突变体（大黑1或d1）及其相应野生型（粳稻日本晴）进行了水稻全转录组微阵列分析（NCBI GEO数据库中的GSE 20925），鉴定出2270个独特的差异表达基因（DEG）。其中，我们使用基因本体术语、STIFDB2.0和水稻数据库挖掘了所有潜在的非生物胁迫响应基因。前两种方法产生的基因子集比在水稻数据库中发现的1886个基因的子集要小。基因本体分析揭示了RGA1突变体中几个胁迫响应基因家族的相似调控。对来自STIFDB的RGA1调控基因的胁迫响应子集进行Genevestigator分析，发现了冷响应和干旱响应簇。水稻数据库的元数据分析揭示了大的胁迫响应类别，如冷胁迫（878个上调/810个下调）、干旱胁迫（882个上调/837个下调）、热胁迫（913个上调/777个下调）和盐胁迫（889个上调/841个下调）。其中1498个基因在所有四种非生物胁迫中都有，其次是在较少胁迫组合中共同出现的基因。RGA1调控的对单个胁迫有独特响应的基因包括热胁迫中的111个、仅冷胁迫和仅干旱胁迫中的各8个以及仅盐胁迫中的2个。共同的差异表达基因（1498个）属于多胺、甘氨酸 - 甜菜碱、脯氨酸和海藻糖合成等途径。一些共同的差异表达基因属于非生物胁迫信号通路，如RGA1突变体中的钙依赖途径、ABA非依赖和依赖途径以及MAP激酶途径。共同的胁迫响应差异表达基因的基因本体揭示了62种独特的分子功能，如转运蛋白、酶调节剂、转移酶、水解酶、碳和蛋白质代谢、与核苷酸、碳水化合物、受体和脂质的结合、形态发生、花发育和细胞稳态。我们还挖掘了63个与本研究中鉴定的胁迫响应转录本结合的miRNA，表明它们的转录后调控作用。总体而言，这些结果表明RGA1在调控水稻多种非生物胁迫方面可能具有广泛作用，有待进一步验证。
